inst/doc/logistic_growth.R

In GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People

## ---- setseed, echo=FALSE-----------------------------------------------------
set.seed(1)
knitr::opts_chunk$set(fig.width = 6, fig.height = 4)
if("package:GillespieSSA" %in% search()) detach("package:GillespieSSA", unload=TRUE) 

## -----------------------------------------------------------------------------
library(GillespieSSA2)
sim_name <- "Pearl-Verhulst Logistic Growth model"
params <- c(b = 2, d = 1, K = 1000)
final_time <- 10
initial_state <- c(N = 500)

## -----------------------------------------------------------------------------
reactions <- list(
  reaction("b * N", c(N = +1)),
  reaction("(d + (b - d) * N / K) * N", c(N = -1))
)

## ----exact--------------------------------------------------------------------
set.seed(1)
out <- ssa(
  initial_state = initial_state,
  reactions = reactions,
  params = params,
  final_time = final_time,
  method = ssa_exact(),
  sim_name = sim_name
) 
plot_ssa(out)

## ----etl----------------------------------------------------------------------
set.seed(1)
out <- ssa(
  initial_state = initial_state,
  reactions = reactions,
  params = params,
  final_time = final_time,
  method = ssa_etl(tau = .03),
  sim_name = sim_name
) 
plot_ssa(out)

## ----btl----------------------------------------------------------------------
set.seed(1)
out <- ssa(
  initial_state = initial_state,
  reactions = reactions,
  params = params,
  final_time = final_time,
  method = ssa_btl(mean_firings = 5),
  sim_name = sim_name
) 
plot_ssa(out)